Workflow

Click the nodes to obtain details about each step.

Quality Check

Step1: Changing Missing IDs

Step2: Removing Multiallelic Variants

Step3: Removing Duplicates

Step4: Variant Missingness Check

Step5: Individual Missingness Check

Step6: Minor Allele Frequency Check

Step7: Hardy-Weinberg Equilibrium Check

Step8: Heterozygosity Check

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
File Code 
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
samples:
  own:  1011GI.vcf.gz
  ref:  1KGP.vcf.gz

population_file: Pop.csv
chromosome: 2
threads:  72

Analysis:
  ADMIXTURE:  False
  SmartPCA: False
  iHS:  False
  XPEHH:  False
  TreeMIX:  False

QualityCheck:
  own:
    geno:  0.02
    mind:  False
    maf:  0.001
    hwe:  1e-6
    heterozygosity:
      StandardDeviations:  3
      LDPruning:
        WindowSize:  1000
        Shift:  10
        CorrelationCoefficient:  0.15
      
  ref:
    geno:  0.02
    mind:  False
    maf:  0.001
    hwe:  1e-6
    heterozygosity:
      StandardDeviations:  False
      LDPruning:
        WindowSize:  1000
        Shift:  10
        CorrelationCoefficient:  0.15

iHS:
  maf:  0.05
  bins:  40
  pop:  ['Adikarnataka' , 'Iyengar' , 'Kolis' , 'Lingayath' , 'Marathas' , 'Deshastha_Brhamin' , 'Konkanastha_brahmin', 'Nadar' , 'Naidu' , 'Namboodari' , 'Parayan' , 'Vakkaliga' , 'Vidiki_Brhamin']
  pop_type:  Pop

  
xpEHH:
  pop: ['OWN']
  reference_pop:  ['AFR' , 'AMR' , 'EAS' , 'EUR' , 'SAS']
  pop_type:  SuperPop
  mapping_pop:  ['OWN']
  bins:  100

ADMIXTURE:
  K:  2
  iterations:  1
  LDPruning:
    WindowSize:  1000
    Shift:  10
    CorrelationCoefficient:  0.15

SmartPCA:
  LDPruning:
    WindowSize:  1000
    Shift:  10
    CorrelationCoefficient:  0.15
  
  Ethnicity_pop: ['OWN']
  pop_type: SuperPop

TreeMIX:
  Root:  YRI
  MigrationEdges:  1
  LDPruning:
    WindowSize:  1000
    Shift:  10
    CorrelationCoefficient:  0.15

Loading...